Upland headwater streams are important sources of freshwater in mountainous temperate to sub-arctic latitude European countries like Scotland. Yet much less is known about the ecology of small, characteristically oligotrophic, mountain streams supporting periphyton and aquatic bryophyte dominated vegetation, and their potential bioindicator capacity of environmental water quality, than lowland rivers impacted by anthropogenic disturbance, in this context. This scarcity of knowledge has significant implications for the success of the recently implemented Water Framework Directive (WFD: 2000/60/EC). The WFD is a major piece of environmental legislation for water policy and sustainable water management in Europe. New contributions are fundamental to environment agencies, such as the Scottish Environment Protection Agency (SEPA), tasked with the responsibility of enforcing WFD statutory requirements and developing effective biomonitoring tools for assessing water quality status in Scotland. A major aim of the WFD is to achieve at least ‘good’ ecological status of inland waterbodies by 2015. Further, in doing so, to ascertain ecological benchmark communities of near-pristine (or minimally-impacted) reference conditions as indicators of high water quality status. The objective is to improve understanding of the environmental processes driving the production and diversity of freshwater plant species-assemblages in upland streams. Such information can be used for assessing perturbations threatening the ecological integrity of rivers impacted by anthropogenic disturbances (human pressure). This enables environment agencies such as SEPA, to respond appropriately by implementing corrective measures and sustainable management strategies. This project monitored a range of near-pristine headwater streams of contrasting underlying geology in the Scottish Highlands. The approach adopted was compatible with current WFD river characterisation and biomonitoring strategies. These were used to investigate the structural and functional response of freshwater plant communities (chiefly diatoms and other algal groups; aquatic bryophyte and vascular submerged macrophyte vegetation) to environmental drivers (e.g. flow, substrate morphology, nutrient inputs, water chemistry, underwater light availability). The work was carried out with the aim of contributing to future development of baseline monitoring tools for assessing upland stream habitat quality in Scotland.